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  • Jan 31 2019 22:37

    bebatut on gh-pages

    Update on: Thu Jan 31 22:36:58 … (compare)

  • Jan 31 2019 22:00

    erasche on master

    Reports fix. Clear up issue in Galaxy docker… More reports fixes... and 1 more (compare)

  • Jan 31 2019 22:00
    erasche closed #1237
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    jmchilton synchronize #1237
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    erasche labeled #1239
  • Jan 31 2019 21:01
    erasche opened #1239
  • Jan 31 2019 21:00
    natefoo opened #1238
  • Jan 31 2019 20:56
    jmchilton opened #1237
  • Jan 31 2019 20:17

    bebatut on gh-pages

    Update on: Thu Jan 31 20:17:17 … (compare)

  • Jan 31 2019 19:44

    erasche on master

    fix typos Merge pull request #1236 from g… (compare)

  • Jan 31 2019 19:44
    erasche closed #1236
  • Jan 31 2019 19:44
    martenson opened #1236
  • Jan 31 2019 19:44

    martenson on martenson-patch-2

    fix typos (compare)

  • Jan 31 2019 19:23

    bebatut on gh-pages

    Update on: Thu Jan 31 19:23:39 … (compare)

  • Jan 31 2019 19:06

    Slugger70 on master

    import some notes fix username and 1 more (compare)

  • Jan 31 2019 19:06
    Slugger70 closed #1234
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    erasche review_requested #1234
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    erasche synchronize #1234
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    erasche unlabeled #1234
Helena Rasche
@hexylena:matrix.org
[m]
https://www.celt.iastate.edu/teaching/effective-teaching-practices/revised-blooms-taxonomy/ from my teacher training, someone added a second dimension to Bloom's, and I kinda like it
1 reply
Helena Rasche
@hexylena:matrix.org
[m]
nice! Thanks for sharing Cristóbal Gallardo
I'm in a course currently to get certified as a higher education instructor, that book might be useful for me the next couple months!
akankshabafna
@akankshabafna
Please could you suggest if I can use Diffbind to compare individual peak files with corresponding treatment and control files coming from 6 different conditions by using " Insert Group". I choose 2 Groups but the " Insert Group" option is greyed out so cannot input any further groups? Is there any better way?
LopezColinas
@LopezColinas
Hello
I wanted to use the goseq tool, but I don't know where to get the gene category for hg19 cells
Does anyone know where I can get the gene category from?
millen2223
@millen2223
@LopezColinas at first glance I don't quite understood what you meant by saying get gene category, please specify a bit more about the problem. Is it tool connected or is this the problem connected with your initial data? As much as I understood from the tool description you only need to specify the UCSC genome/ID in most cases. If you mean GO categories to genes, the documentation says it should automatically retrieve mapping between these categories for commonly used genome/ID combinations. In any other case tools says that "if your genome is not available, you will also need a file describing the membership of genes in categories. The category file should have two columns with an optional header row. with Gene ID in the first column and category identifier in the second column".
Helge Hecht
@hechth
Hi all! I just wanted to ask if there are any tutorials/trainings on how to generate things from the built-in visualizations or how they work, how to create Galaxy pages or visualizations for workflow reports?
Helena Rasche
@hexylena:matrix.org
[m]
there are currently no tutorials on writing workflow reports but we'd love to have one
unfortunately no one has had time to write it yet
but the workflow report editor is quite easy to use I think, please let us know if you have any questions while using it
millen2223
@millen2223
@hexylena:matrix.org I found this video which reminded me of the topic, I haven't done workflows reports yet. Have you discussed with @hechth a report like this one? https://www.youtube.com/watch?v=TmZzfaKf1V0
Helena Rasche
@hexylena:matrix.org
[m]
yes! that's the new interface, it should be very easy to create a report with it, if you have an idea of what you want to be in your WF report
millen2223
@millen2223
Wow, now I see. I get more and more surprised in a good way how fast changes here happen. The concept with WF and reports looks very convenient for a user
Wendi Bacon
@nomadscientist
Ohhh I’m loving the ‘add contributions’ button, very nice
1 reply
niraito
@niraito
"Hello,
I was following the tutorial at Protein-ligand docking 4.
I am not able to visualize my results as per the tutorial and as per attachment using NGL Viewer.
Can you please help me?
regards
Preenon Bagchi" https://help.galaxyproject.org/t/protein-ligand-docking-visualization-using-nglviewer/6194
I am having the same problem :(
this is the first time that I use gitter, it would be so nice if anybody help me about it :pray:
Simon Bray
@simonbray:matrix.org
[m]
Hi @niraito I added my answer to that thread
Let me know if you have any other questions
niraito
@niraito
Thank you very much! :pray:
david wills
@davidwi23009754_twitter
how do delet apps from my phone
akankshabafna
@akankshabafna
@jennaj Please could you suggest if I can use Diffbind to compare individual peak files with corresponding treatment and control files coming from 6 different conditions by using " Insert Group". I choose 2 Groups but the " Insert Group" option is greyed out so cannot input any further groups? Is there any better way?
david wills
@davidwi23009754_twitter
how do i delit apps from my phone
bgruening
@bgruening:matrix.org
[m]
@davidwi23009754_twitter: you are in the wrong channel. This channel has nothing to do with mobile phones.
akankshabafna
@akankshabafna

@bgruening Hi,
I am using Diffbind to compare H3K27ac peaks between two time points. Recently, we added 4 more time points to the existing 2 to do time-series comparison.
From my understanding, Diffbind could conventionally compare and provide differential bound sites between 2 samples .

Q1: Is there a way to compare and contrast 6 time-points, considering each has 2 biological replicates.
Q2 If the answer to Q1 is no, when I compare A to B and separately A to C , why do I get different counts for A in the binding affinity matrix arising from A vs B to A vs C for the same peak interval.

Ali Sajid Imami
@asimami:matrix.org
[m]
Ohaio Everyone.
Is this where the papercuts for GTN people are meeting?
millen2223
@millen2223:matrix.org
[m]
Ali Sajid ImamiDo you mean this one? Papercuts Call 3: Americas
12:00 US ?
Ali Sajid Imami
@asimami:matrix.org
[m]
No. There was one supposed to be at 11 Eastern time.
I joined but there was no one there.
I've started goign through issues and working on them though.
millen2223
@millen2223:matrix.org
[m]
Ali Sajid ImamiI see, I didn't attend this one, so unfortunately, I can't say what happened. Definitely it's great that you are working on issues as it's a significant part of paper cuts event👍️. This channel is also a place where you can ask questions
Basilio Cieza Huaman
@bciezah1
Hi guys, I have questions. I have been using the Galaxy Australia (metatranscriptomics -extended version), and I found that in the section "Regroup HUMAnN table features", galaxy did not allow to select the option:
“Mapping to use for the grouping”: Mapping (full) for Gene Ontology (GO) from UniRef90" if anyone had the same issue? Thanks in advance.
lmakeke29
@lmakeke29
hi
how do i contact admins?
lmakeke29
@lmakeke29
how can i get gpu enabled notebooks??
bgruening
@bgruening:matrix.org
[m]
@lmakeke29: for what do you need that?
GPU are expensive and get abused a lot, so we are hesitant to give them out.
Saskia Hiltemann
@shiltemann:matrix.org
[m]
Regarding the GTN Video Library (see post by the bot above): if you are an instructor and you have recorded a video, and it is not available from the corresponding GTN tutorial as described above, please let us know and we will fix/add it!
GTN Bot
@gtn-bot:matrix.org
[m]

GTN News for Nov 25

Big News!

4 new contributors!

Helena Rasche
@hexylena:matrix.org
[m]
urgh, some duplicates. I guess my git diff line is wrong then.
GTN Bot
@gtn-bot:matrix.org
[m]

GTN News for Nov 30

1 new tutorials!

Helena Rasche
@hexylena:matrix.org
[m]
really need to fix that pluralisation huh
Wendi Bacon
@nomadscientist
All these beautiful automations just poking you in the eye :(
Helena Rasche
@hexylena:matrix.org
[m]
I wrote it in a silly way, it's my fault. I used git to tell me what changes were done in the last 24h and I really should've done it the proper way by storing somewhere the commit it last ran at.
laziness
Jessica Conway
@jessicaconway__twitter
Hi, what taxlevel (taxonomy level for split) is for OTU clustering at the phylum level?
1 reply
M Bernt
@bernt-matthias:matrix.org
[m]
Does someone know why in the mothur tutorial silva is used for alignment and rdp for taxonomic classification?